Identification and classification of antiviral defence systems in bacteria and archaea with PADLOC reveals new system types

Abstract

To provide protection against viral infection and limit the uptake of mobile genetic elements, bacteria and archaea have evolved many diverse defence systems. The discovery and application of CRISPR-Cas adaptive immune systems has spurred recent interest in the identification and classification of new types of defence systems. Many new defence systems have recently been reported but there is a lack of accessible tools available to identify homologs of these systems in different genomes. Here, we report the Prokaryotic Antiviral Defence LOCator (PADLOC), a flexible and scalable open-source tool for defence system identification. With PADLOC, defence system genes are identified using HMM-based homologue searches, followed by validation of system completeness using gene presence/absence and synteny criteria specified by customisable system classifications. We show that PADLOC identifies defence systems with high accuracy and sensitivity. Our modular approach to organising the HMMs and system classifications allows additional defence systems to be easily integrated into the PADLOC database. To demonstrate application of PADLOC to biological questions, we used PADLOC to identify six new subtypes of known defence systems and a putative novel defence system comprised of a helicase, methylase and ATPase. PADLOC is available as a standalone package (https://github.com/padlocbio/padloc) and as a webserver (https://padloc.otago.ac.nz).

A Comparative Analysis of Weizmannia coagulans Genomes Unravels the Genetic Potential for Biotechnological Applications

“…Identification of prokaryotic innate defense systems in the W. coagulans genomes was carried out using the webtool PADLOC ( , accessed on 16 September 2021) [ 86 ]. CRISPR/Cas systems were identified with the web tool CRISPRCasTyper ( , accessed on 15 September 2021) [ 87 ] and the orientation of the CRISPR arrays was determined using CRISPRDetect ( , accessed on 15 September 2021).…”

Efficacy of plasmid-encoded CRISPR-Cas antimicrobial is affected by competitive factors found in wildEnterococcus faecalisisolates

“…To identify CRISPR loci and cas genes the web tool CRISPRCasFinder was utilized with manual verification (55, 56). Searches for anti-plasmid defense systems anti-CRISPR and Wadjet were done using the AcrDB (57) and PADLOC (34) respectively. Bacteriocins were identified using the BAGEL4 web server (58) (Table S1).…”

Metagenomic Assessment of DNA Viral Diversity in Freshwater Sponges, Baikalospongia bacillifera

“…In our study, we analyzed whether these strains have any antiviral defense mechanisms. To search for defense mechanisms, we analyzed bacterial genomes using the Prokaryotic Antiviral Defense LOCator (PADLOC) [65] and CRISPRCasFinder [66] algorithms, and the numbers of CRISPR arrays were detected. Spacers' sequences were aligned with viral scaffolds from our study using the BLASTn-short algorithm [49], as recommended in [67].…”

“…strain SLB01 and Flavobacterium sp. Strain SLB02 from the Baikal sponge Lubomirskia baikalensis [64] revealed seven variants of CRISPR-Cas spacers (one in SLB01 and six in SLB02) and five other types of antiphage defense systems, including recently discovered [65,69] (dGTPase, Zorya_type I, Septu_type I, Gabija, Cbass_type III) (Supplementary Tables S4 and S5, File S3). The 14 matches of CRISPR-Cas spacers from Strain SLB02 and SLB01 were found with 13 different viral scaffolds from the sponge B. bacillifera (Supplementary File S4).…”